y_petri 2.1.9 → 2.1.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: d3b852100353e1df976a7c8f3ffd84e0cd2c6dce
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+  data.tar.gz: 473f087960a3a4ed4b93cb2bef5262f0a4e8268e
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data/lib/y_petri/agent/simulation_related.rb

@@ -280,26 +280,68 @@ module YPetri::Agent::SimulationRelated
              title: "Selected features plot", ylabel: "Marking" )
   end
 
-  # Plot the recorded samples (system state history).
+  # Plot system state history.
   # 
-  def plot_state( place_ids=nil, except: [] )
-    sim = simulation or return nil
-    rec = sim.recording
-    pp = sim.net.pp( place_ids.nil? ? net.pp : place_ids  ) -
-      sim.net.pp( except )
-    dataset = sim.recording.reduce_features( marking: pp )
-    dataset.plot
+  def plot_state( place_ids=nil, except: [],
+                  title: "State plot", ylabel: "Marking [µM]",
+                  **options )
+    rec = simulation.recording
+    pp = simulation.pp( place_ids ) - simulation.pp( except )
+    rec.marking( pp ).plot( title: title, ylabel: ylabel, **options )
   end
   alias plot_marking plot_state
 
-  # Plot the recorded flux (computed flux history at the sampling points).
+  # Plot flux history of TS transitions.
   # 
-  def plot_flux( transition_ids=nil, except: [], **options )
-    sim = simulation or return nil
-    rec = sim.recording
-    tt = sim.net.tt( transition_ids.nil? ? net.tt : transition_ids ) -
-      sim.net.tt( except )
-    dataset = sim.recording.reduce_features( flux: tt )
-    dataset.plot( title: "Flux plot", ylabel: "Flux [µMⁿ.s⁻¹]" )
+  def plot_flux( transition_ids=nil, except: [],
+                 title: "Flux plot", ylabel: "Flux [µM.s⁻¹]",
+                 **options )
+    rec = simulation.recording
+    tt = transition_ids.nil? ? simulation.TS_tt : transition_ids
+    tt = simulation.TS_tt( tt )
+    tt -= simulation.tt( except )
+    rec.flux( tt ).plot( title: title, ylabel: ylabel, **options )
+  end
+
+  # Plot firing history of tS transitions.
+  # 
+  def plot_firing( transition_ids=nil, except: [],
+                   title: "Firing plot", ylabel: "Firing [µM]",
+                   **options )
+    rec = simulation.recording
+    tt = transition_ids.nil? ? simulation.tS_tt : transition_ids
+    tt = simulation.tS_tt( tt )
+    tt -= simulation.tt( except )
+    rec.firing( tt ).plot( title: title, ylabel: ylabel, **options )
+  end
+
+  # Plot gradient history of selected places with respect to a set of T
+  # transitions.
+  # 
+  def plot_gradient( place_ids=nil, except: [], transitions: nil,
+                     title: "Gradient plot", ylabel: "Gradient [µM.s⁻¹]",
+                     **options )
+    rec = simulation.recording
+    pp = simulation.pp( place_ids ) - simulation.ee( place_ids )
+    tt = transitions.nil? ? simulation.T_tt : transitions
+    tt = simulation.T_tt( tt )
+    tt -= simulation.ee( except )
+    rec.gradient( pp, transitions: tt )
+      .plot( title: title, ylabel: ylabel, **options )
+  end
+
+  # Plot delta history of selected places with respect to a set of transitions.
+  # 
+  def plot_delta( place_ids=nil, except: [], transitions: nil,
+                  title: "Delta plot", ylabel: "Delta [µM]",
+                  **options )
+    options.may_have :delta_time, syn!: :Δt
+    rec = simulation.recording
+    pp = simulation.pp( place_ids ) - simulation.ee( except )
+    tt = transitions.nil? ? simulation.tt : tranisitions
+    tt = simulation.tt( tt )
+    tt -= simulation.ee( except )
+    rec.delta( pp, transitions: tt, delta_time: options[:delta_time] )
+      .plot( title: title, ylabel: ylabel, **options )
   end
 end # module YPetri::Agent::SimulationRelated

data/lib/y_petri/net/data_set.rb

@@ -198,7 +198,7 @@ class YPetri::Net::DataSet < Hash
     else
       return reduce_features net.State.delta if args.empty?
       reduce_features delta: args
-    end      
+    end
   end
 
   # Outputs the current recording in CSV format.

data/lib/y_petri/net/element_access.rb

@@ -32,7 +32,7 @@ module YPetri::Net::ElementAccess
       fail TypeError, "No place #{id} in the net!" unless places.include? p
     end
   end
-  
+
   # Returns the net's transition identified by the argument.
   # 
   def transition id

data/lib/y_petri/net/state/feature/delta.rb

@@ -11,12 +11,12 @@ class YPetri::Net::State::Feature::Delta < YPetri::Net::State::Feature
         # First, prepare the hash of instances.
         hsh = Hash.new do |ꜧ, id|
           if id.is_a? self then # missing key "id" is a Delta instance
-            ꜧ[ [ id.place, transitions: id.transitions.sort( &:object_id ) ] ]
+            ꜧ[ [ id.place, transitions: id.transitions.sort_by( &:object_id ) ] ]
           else
             p = id.fetch( 0 )
             tt = id.fetch( 1 ).fetch( :transitions ) # value of :transitions key
             if p.is_a? ç.net.Place and tt.all? { |t| t.is_a? ç.net.Transition }
-              if tt == tt.sort then
+              if tt == tt.sort_by( &:object_id ) then
                 # Cache the instance.
                 ꜧ[ id ] = if tt.all? &:timed? then
                             ç.timed( *id )
@@ -28,7 +28,7 @@ class YPetri::Net::State::Feature::Delta < YPetri::Net::State::Feature
                               "all timed, or all timeless!"
                           end
               else
-                ꜧ[ [ p, transitions: tt.sort ] ]
+                ꜧ[ [ p, transitions: tt.sort_by( &:object_id ) ] ]
               end
             else # convert place and transition ids to places and transitions
               ꜧ[ [ ç.net.place( p ), transitions: ç.net.transitions( tt ) ] ]
@@ -48,7 +48,14 @@ class YPetri::Net::State::Feature::Delta < YPetri::Net::State::Feature
     # transition identifiers supplied as +:transitions: parameter.
     # 
     def timed place, transitions: net.T_tt
-      __new__( place, transitions: net.T_tt( transitions ) )
+      tt = begin
+             net.T_tt( transitions )
+           rescue TypeError => err
+             msg = "Transitions #{transitions} not recognized as timed " +
+               "transitions in #{net}! (%s)"
+             raise TypeError, msg % err
+           end
+      __new__( place, transitions: tt )
         .tap { |inst| inst.instance_variable_set :@timed, true }
     end
 
@@ -56,6 +63,13 @@ class YPetri::Net::State::Feature::Delta < YPetri::Net::State::Feature
     # timeless transition identifiers as +:transitions: parameter.
     # 
     def timeless place, transitions: net.t_tt
+      tt = begin
+             net.t_tt( transitions )
+           rescue TypeError => err
+             msg = "Transitions #{transitions} not recognized as timed " +
+               "transitions in #{net}! (%s)"
+             raise TypeError, msg % err
+           end
       __new__( place, transitions: net.t_tt( transitions ) )
         .tap { |inst| inst.instance_variable_set :@timed, false }
     end

data/lib/y_petri/net/state/feature/firing.rb

@@ -14,7 +14,15 @@ class YPetri::Net::State::Feature::Firing < YPetri::Net::State::Feature
                                    when self then
                                      hsh[ id.transition ]
                                    when ç.net.Transition then
-                                     hsh[ id ] = ç.__new__( id )
+                                     t = begin
+                                           ç.net.tS_transitions( [ id ] ).first
+                                         rescue TypeError => err
+                                           msg = "Transition #{id} not " +
+                                             "recognized as tS transition in " +
+                                             "net #{ç.net}! (%s)"
+                                           raise TypeError, msg % err
+                                         end
+                                     hsh[ id ] = ç.__new__( t )
                                    else
                                      hsh[ ç.net.transition( id ) ]
                                    end
@@ -42,7 +50,7 @@ class YPetri::Net::State::Feature::Firing < YPetri::Net::State::Feature
   def extract_from arg, **nn
     case arg
     when YPetri::Simulation then
-      arg.send( :tS_transitions, [ transition ] ).firing.first
+      arg.send( :tS_transitions, [ transition ] ).first.firing
     else
       fail TypeError, "Argument type not supported!"
     end

data/lib/y_petri/net/state/feature/flux.rb

@@ -14,7 +14,15 @@ class YPetri::Net::State::Feature::Flux < YPetri::Net::State::Feature
                                    when self then
                                      hsh[ id.transition ]
                                    when ç.net.Transition then
-                                     hsh[ id ] = ç.__new__( id )
+                                     t = begin
+                                           ç.net.TS_transitions( [ id ] ).first
+                                         rescue TypeError => err
+                                           msg = "Transition #{id} not " +
+                                             "recognized as TS transition in " +
+                                             "net #{ç.net}! (%s)"
+                                           raise TypeError, msg % err
+                                         end
+                                     hsh[ id ] = ç.__new__( t )
                                    else
                                      hsh[ ç.net.transition( id ) ]
                                    end
@@ -42,7 +50,7 @@ class YPetri::Net::State::Feature::Flux < YPetri::Net::State::Feature
   def extract_from arg, **nn
     case arg
     when YPetri::Simulation then
-      arg.send( :TS_transitions, [ transition ] ).flux.first
+      arg.send( :TS_transitions, [ transition ] ).first.flux
     else
       fail TypeError, "Argument type not supported!"
     end

data/lib/y_petri/net/state/feature/gradient.rb

@@ -11,17 +11,25 @@ class YPetri::Net::State::Feature::Gradient < YPetri::Net::State::Feature
         # First, prepare the hash of instances.
         hsh = Hash.new do |ꜧ, id|
           if id.is_a? self then
-            ꜧ[ [ id.place, transitions: id.transitions.sort( &:object_id ) ] ]
+            ꜧ[ [ id.place, transitions: id.transitions.sort_by( &:object_id ) ] ]
           else
             p = id.fetch( 0 )
             tt = id
               .fetch( 1 )
               .fetch( :transitions )
             if p.is_a? ç.net.Place and tt.all? { |t| t.is_a? ç.net.Transition }
-              if tt == tt.sort then
+              tt_sorted = tt.sort_by &:object_id
+              if tt == tt_sorted then
+                tt = begin
+                       ç.net.T_transitions( tt )
+                     rescue TypeError => err
+                       msg = "Transitions #{tt} not recognized as T " +
+                         "transitions in net #{ç.net}! (%s)"
+                       raise TypeError, msg % err
+                     end
                 ꜧ[ id ] = ç.__new__( *id )
               else
-                ꜧ[ [ p, transitions: tt.sort ] ]
+                ꜧ[ [ p, transitions: tt.sort_by( &:object_id ) ] ]
               end
             else
               ꜧ[ [ ç.net.place( p ), transitions: ç.net.transitions( tt ) ] ]

data/lib/y_petri/net/state/feature/marking.rb

@@ -14,6 +14,13 @@ class YPetri::Net::State::Feature::Marking < YPetri::Net::State::Feature
                                    when self then
                                      hsh[ id.place ]
                                    when ç.net.Place then
+                                     p = begin
+                                           ç.net.place id
+                                         rescue TypeError => err
+                                           msg = "Place #{id} not recognized " +
+                                             "a place in net #{ç.net}! (%s)"
+                                           raise TypeError, msg % err
+                                         end
                                      hsh[ id ] = ç.__new__( id )
                                    else
                                      hsh[ ç.net.place( id ) ]

data/lib/y_petri/net/state/feature.rb

@@ -49,7 +49,9 @@ class YPetri::Net::State::Feature
       when Gradient() then id
       when Gradient then
         Gradient().of( id.place, transitions: id.transitions )
-      else Gradient().of( id, transitions: transitions ) end # assume it's a place
+      else
+        Gradient().of( id, transitions: transitions )
+      end # assume it's a place
     end
 
     def Flux id=L!
@@ -57,7 +59,9 @@ class YPetri::Net::State::Feature
       case id
       when Flux() then id
       when Flux then Flux().of( id.transition )
-      else Flux().of( id ) end # assume it's a place
+      else
+        Flux().of( id )
+      end # assume it's a place
     end
 
     def Delta id=L!, transitions: net.tt

data/lib/y_petri/net.rb

@@ -1,4 +1,4 @@
-#encoding: utf-8
+# encoding: utf-8
 
 require_relative 'net/element_access'
 require_relative 'net/visualization'

data/lib/y_petri/simulation/elements/access.rb

@@ -22,7 +22,7 @@ class YPetri::Simulation::Elements
     # Elements of the simulation (belonging to the net).
     # 
     def ee( ids=nil )
-      elements( ids ).sources
+      elements( ids ).map &:source
     end
 
     # Names of the simulation's elements. Arguments, if any, are treated

data/lib/y_petri/simulation/transition_representation/TS.rb

@@ -1,4 +1,4 @@
-#encoding: utf-8
+# encoding: utf-8
 
 # A mixin for TS transition representations.
 # 
@@ -6,16 +6,16 @@ class YPetri::Simulation::TransitionRepresentation
   module Type_TS
     include Type_T
     include Type_S
-    
+
     attr_reader :rate_closure
-    
+
     # Initialization subroutine.
     # 
     def init
       super
       @rate_closure = to_rate_closure
     end
-    
+
     # Transition's rate, given the current system state.
     # 
     def rate
@@ -23,20 +23,20 @@ class YPetri::Simulation::TransitionRepresentation
     end
     alias flux rate
     alias propensity rate
-    
+
     # Firing of the transition (rate * Δtime).
     # 
     def firing Δt
       rate * Δt
     end
-    
+
     # Gradient contribution of the transition to all places.
     # 
     def ∇
       codomain >> stoichiometry.map { |coeff| rate * coeff }
     end
     alias gradient_all ∇
-    
+
     # Builds a flux closure.
     # 
     def to_rate_closure

data/lib/y_petri/simulation/transitions/TS.rb

@@ -1,4 +1,4 @@
-#encoding: utf-8
+# encoding: utf-8
 
 # Mixin for collections of TS transitions.
 #

data/lib/y_petri/version.rb

@@ -1,4 +1,4 @@
 module YPetri
-  VERSION = "2.1.9"
+  VERSION = "2.1.10"
   DEBUG = false
 end

data/lib/y_petri.rb

@@ -1,4 +1,4 @@
-#encoding: utf-8
+# encoding: utf-8
 
 require 'active_support/core_ext/module/delegation'
 require 'active_support/core_ext/array/extract_options'

data/test/agent_test.rb

@@ -1,5 +1,5 @@
 #! /usr/bin/ruby
-# -*- coding: utf-8 -*-
+# encoding: utf-8
 
 gem 'minitest', '=4.7.4'
 require 'minitest/autorun'
@@ -11,7 +11,7 @@ describe YPetri::Agent do
   before do
     @m = YPetri::Agent.new
   end
-  
+
   it "has net basic points" do
     # --- net point related assets ---
     @m.net_point_reset
@@ -68,7 +68,7 @@ describe YPetri::Agent do
     @m.tn.must_equal []
     @m.nn.must_equal [ :Top ]       # ie. :Top net spanning whole workspace
   end
-  
+
   describe "slightly more complicated case" do
     before do
       @p = @m.Place ɴ: "P", default_marking: 1
@@ -81,7 +81,7 @@ describe YPetri::Agent do
       @m.set_sampling 1
       @m.set_time 0..30
     end
-    
+
     it "works" do
       @m.run!
       @m.simulation.send( :places ).map( &:source )
@@ -97,6 +97,15 @@ describe YPetri::Agent do
         .stoichiometry_matrix.row_size.must_equal 2
       @m.simulation.flux_vector.row_size.must_equal 2
       # @m.plot_recording
+      rec = @m.simulation.recording
+      rec.marking.plot
+      rec.flux.plot
+      rec.gradient.plot
+      rec.delta( Δt: 1 ).plot
+      @m.plot_marking
+      @m.plot_flux
+      @m.plot_gradient
+      @m.plot_delta( Δt: 1 )
     end
   end
 end

data/test/simulation_test.rb

@@ -288,9 +288,9 @@ describe "timeless simulation" do
     ds.firing.slice( 1..2 ).series
       .must_equal [[1, 1]]
     ds.series( firing: [:U2V] )
-      .must_equal [[1, 1, 1, 1, 1, 1]]
+      .must_equal [ [ 1, 1, 1, 1, 1, 1 ] ]
     ds.delta( [:U], transitions: [:Uplus] ).series
-      .must_equal [[1.0, 1.0, 1.0, 1.0, 1.0, 1.0]]
+      .must_equal [ [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0 ] ]
     tmp = ds.reduce_features( marking: [:U], firing: [:U2V] )
     tmp.features
       .must_equal( ds.net.State.features marking: [:U], firing: [:U2V] )

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: y_petri
 version: !ruby/object:Gem::Version
-  version: 2.1.9
+  version: 2.1.10
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-10 00:00:00.000000000 Z
+date: 2013-08-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: y_support